In vitro, long-range sequence information for de novo genome assembly via transposase contiguity
- Andrew Adey1,
- Jacob O Kitzman1,
- Joshua N Burton1,
- Riza Daza1,
- Akash Kumar1,
- Lena Christiansen2,
- Mostafa Ronaghi2,
- Sasan Amini2,
- Kevin Gunderson2,
- Frank J Steemers2 and
- Jay Shendure1,3
- ↵* Corresponding author; email: shendure{at}uw.edu
Abstract
We describe a method that exploits contiguity preserving transposase sequencing (CPT-seq) to facilitate the scaffolding of de novo genome assemblies. CPT-seq is an entirely in vitro means of generating libraries comprised of 9,216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to over 1 megabase. These pools are 'sub-haploid', in that the lengths of fragments contained in each pool sums to approximately 5 to 10% of the full genome. The scaffolding approach described here, termed fragScaff, leverages coincidences between the content of different pools as a source of contiguity information. Specifically, CPT-seq data is mapped to a de novo genome assembly, followed by the identification of pairs of contigs or scaffolds whose ends disproportionately co-occur in the same indexed pools, consistent with true adjacency in the genome. Such candidate 'joins' are used to construct a graph, which is then resolved by a minimum spanning tree. As a proof-of-concept, we apply CPT-seq and fragScaff to substantially boost the contiguity of de novo assemblies of the human, mouse, and fly genomes, increasing the scaffold N50 of de novo assemblies by 8 to 57 fold with high accuracy. We also demonstrate that fragScaff is complementary to Hi-C-based contact probability maps, providing mid-range contiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps. Finally, we demonstrate CPT-seq as a means of anchoring unplaced novel human contigs to the reference genome as well as for detecting misassembled sequences.
- Received May 13, 2014.
- Accepted August 4, 2014.
- Published by Cold Spring Harbor Laboratory Press
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